Salmonella enterica serovar Typhimurium. Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Salmonella enterica subsp. enterica serovar Typhimurium str. D23580. Whereas most non-typhoidal Salmonella (NTS) are associated with gastroenteritis there has been a dramatic increase in reports of NTS-associated invasive disease in Sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multi locus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, currently rarely reported outside Africa. Whole genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared to other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologues in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for micro-evolution and clonal replacement in the field.